rename function build_update_taxonomy (#127)

rename function `build_update_taxonomy` to `dataset_update_taxonomy` to align with naming conventions. This function updates taxonomy of 1 dataset at a time
traitecoevo · Nov 15, 2023 · 27ecb28 · 27ecb28
1 parent d0b132e
commit 27ecb28
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Showing 10 changed files with 17 additions and 17 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,14 +4,14 @@ export("%>%")
 export(build_add_version)
 export(build_combine)
 export(build_setup_pipeline)
-export(build_update_taxonomy)
 export(check_duplicates)
 export(dataset_build)
 export(dataset_configure)
 export(dataset_find_taxon)
 export(dataset_process)
 export(dataset_report)
 export(dataset_test)
+export(dataset_update_taxonomy)
 export(get_schema)
 export(get_unit_conversions)
 export(metadata_add_contexts)

diff --git a/R/process.R b/R/process.R
@@ -279,7 +279,7 @@ dataset_process <- function(filename_data_raw,
 #' Build dataset
 #'
 #' Build specified dataset. This function completes three steps, which can be executed separately if desired:
-#' `dataset_configure`, `dataset_process`, `build_update_taxonomy`
+#' `dataset_configure`, `dataset_process`, `dataset_update_taxonomy`
 #'
 #' @param filename_metadata Metadata yaml file for a given study
 #' @param filename_data_raw Raw `data.csv` file for any given study
@@ -319,7 +319,7 @@ dataset_build <- function(
   dataset_raw <- dataset_process(
     filename_data_raw, dataset_config, schema, resource_metadata, unit_conversion_functions,
     filter_missing_values = filter_missing_values)
-  dataset <- build_update_taxonomy(dataset_raw, taxon_list)
+  dataset <- dataset_update_taxonomy(dataset_raw, taxon_list)
 
   dataset
 }
@@ -1860,7 +1860,7 @@ build_combine <- function(..., d = list(...)) {
 #' @importFrom rlang .data
 #'
 #' @export
-build_update_taxonomy <- function(austraits_raw, taxa) {
+dataset_update_taxonomy <- function(austraits_raw, taxa) {
 
   columns_in_taxon_list <- names(taxa)
 

diff --git a/R/testdata.R b/R/testdata.R
@@ -327,8 +327,8 @@ dataset_test_worker <-
       }, info = "`dataset_process`")
 
       expect_no_error({
-        build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list)
-      }, info = "`build_update_taxonomy`")
+        build_dataset <- dataset_update_taxonomy(build_dataset_raw, taxon_list)
+      }, info = "`dataset_update_taxonomy`")
 
       build_dataset
     }

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -34,7 +34,7 @@ reference:
     - '`build_setup_pipeline`'
     - '`build_combine`'
     - '`build_add_version`'
-    - '`build_update_taxonomy`'
+    - '`dataset_update_taxonomy`'
     - '`dataset_build`'
     - '`dataset_configure`'
     - '`dataset_process`'

diff --git a/inst/support/build_base.whisker b/inst/support/build_base.whisker
@@ -16,7 +16,7 @@ taxon_list <- read_csv_char("config/taxon_list.csv")
 {{#dataset_ids}}
 {{dataset_id}}_config <- dataset_configure("{{path}}/{{dataset_id}}/metadata.yml", definitions)
 {{dataset_id}}_raw <- dataset_process("{{path}}/{{dataset_id}}/data.csv", {{dataset_id}}_config, schema, resource_metadata, unit_conversions)
-{{dataset_id}} <- build_update_taxonomy({{dataset_id}}_raw, taxon_list)
+{{dataset_id}} <- dataset_update_taxonomy({{dataset_id}}_raw, taxon_list)
 
 {{/dataset_ids}}
 

diff --git a/inst/support/build_remake.whisker b/inst/support/build_remake.whisker
@@ -46,7 +46,7 @@ targets:
                  )
   {{dataset_id}}:
     command: >
-      build_update_taxonomy({{dataset_id}}_raw,
+      dataset_update_taxonomy({{dataset_id}}_raw,
                   taxon_list
                  )
 

diff --git a/man/dataset_build.Rd b/man/dataset_build.Rd
diff --git a/man/build_update_taxonomy.Rd → man/dataset_update_taxonomy.Rd b/man/build_update_taxonomy.Rd → man/dataset_update_taxonomy.Rd
diff --git a/tests/testthat/functions.R b/tests/testthat/functions.R
@@ -107,8 +107,8 @@ test_build_dataset <- function(
   }, info = paste(info, "`dataset_process`"))
 
   expect_no_error({
-    build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list)
-  }, info = paste(info, "`build_update_taxonomy`"))
+    build_dataset <- dataset_update_taxonomy(build_dataset_raw, taxon_list)
+  }, info = paste(info, "`dataset_update_taxonomy`"))
 
   test_structure(build_dataset, info, schema, definitions, single_dataset = TRUE)
 

diff --git a/tests/testthat/test-setup.R b/tests/testthat/test-setup.R
@@ -666,8 +666,8 @@ test_that("`build_setup_pipeline` is working", {
   expect_equal(austraits$build_info$git_SHA, sha)
   expect_equal(austraits$build_info$git_SHA, "6c73238d8d048781d9a4f5239a03813be313f0dd")
 
-  #expect_length(austraits_raw$taxa, 14) #not valid test with new `build_update_taxonomy setup`
-  #expect_length(austraits$taxa, 14) #not valid test with new `build_update_taxonomy setup`
+  #expect_length(austraits_raw$taxa, 14) #not valid test with new `dataset_update_taxonomy setup`
+  #expect_length(austraits$taxa, 14) #not valid test with new `dataset_update_taxonomy setup`
   expect_equal(nrow(austraits$taxa), nrow(austraits_raw$taxa))
 
   # Compare products from three methods, except `build_info`